# HG changeset patch
# User iuc
# Date 1697625779 0
# Node ID 2dccb6bb0addc34817928c044a1faa846999f6bd
# Parent aeacaf08bd521fc945f4dcb9049ce5a1274700c9
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/hicexplorer commit 07802a6bd441d9da888cfb8283f8c2135704f7c9
diff -r aeacaf08bd52 -r 2dccb6bb0add hicAdjustMatrix.xml
--- a/hicAdjustMatrix.xml Tue Jan 10 19:05:09 2023 +0000
+++ b/hicAdjustMatrix.xml Wed Oct 18 10:42:59 2023 +0000
@@ -25,11 +25,15 @@
--regions '$chromosomeOrRegionFile_conditional.regions'
#end if
+ #if not $interIntra_selector == 'keep':
+ --interIntraHandling $interIntra_selector
+ #end if
&& mv '$matrix_file_out' matrix
+
]]>
-
+
@@ -51,6 +55,11 @@
+
+
+
+
+
@@ -64,15 +73,15 @@
-
+
-
-
+
+
@@ -80,12 +89,12 @@
-
-
+
+
diff -r aeacaf08bd52 -r 2dccb6bb0add macros.xml
--- a/macros.xml Tue Jan 10 19:05:09 2023 +0000
+++ b/macros.xml Wed Oct 18 10:42:59 2023 +0000
@@ -1,7 +1,7 @@
\${GALAXY_SLOTS:-4}
- 3.6
- 1
+ 3.7.2
+ 0
#if $use_range.select_use_range == "yes_use_range":
--range $use_range.range_min:$use_range.range_max
@@ -37,7 +37,8 @@
- 10.5281/zenodo.1133705
+ 10.1093/nar/gkaa220
+ 10.1093/nar/gky504
@@ -348,6 +349,10 @@
+
+
+
+
@@ -356,6 +361,8 @@
+
+
@@ -377,9 +384,17 @@
-
+
+
+
+
+
+ value.replace(' ', '').isnumeric()
+
+
+
@@ -390,6 +405,9 @@
+
+
+
@@ -408,6 +426,14 @@
+
+
+
+
+ value.replace(' ', '').isnumeric()
+
+
+
@@ -418,6 +444,8 @@
+
+
@@ -426,6 +454,7 @@
+
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/cHi-C/aggregate.tar.gz
Binary file test-data/cHi-C/aggregate.tar.gz has changed
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_FL-E13-5_chr1_chr1_Eya1_aggregate.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_FL-E13-5_chr1_chr1_Eya1_aggregate.txt Wed Oct 18 10:42:59 2023 +0000
@@ -0,0 +1,9 @@
+# Chromosome Start End Gene Sum of interactions Relative position Raw
+chr1 14274000 14278000 Eya1 673.000000000000 -23000 5.600000000000
+chr1 14295000 14298000 Eya1 673.000000000000 -3000 44.400000000000
+chr1 14314000 14319000 Eya1 673.000000000000 18000 24.200000000000
+chr1 14426000 14432000 Eya1 673.000000000000 131000 2.400000000000
+chr1 14447000 14455000 Eya1 673.000000000000 154000 4.400000000000
+chr1 14460000 14465000 Eya1 673.000000000000 164000 3.200000000000
+chr1 14480000 14488000 Eya1 673.000000000000 187000 7.600000000000
+chr1 14491000 14501000 Eya1 673.000000000000 200000 20.650000000000
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_FL-E13-5_chr1_chr1_Sox17_aggregate.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_FL-E13-5_chr1_chr1_Sox17_aggregate.txt Wed Oct 18 10:42:59 2023 +0000
@@ -0,0 +1,9 @@
+# Chromosome Start End Gene Sum of interactions Relative position Raw
+chr1 4481000 4488000 Sox17 810.000000000000 0 297.800000000000
+chr1 4499000 4502000 Sox17 810.000000000000 14000 20.400000000000
+chr1 4509000 4515000 Sox17 810.000000000000 27000 27.800000000000
+chr1 4561000 4567000 Sox17 810.000000000000 79000 11.600000000000
+chr1 4585000 4590000 Sox17 810.000000000000 102000 8.000000000000
+chr1 4652000 4658000 Sox17 810.000000000000 170000 6.000000000000
+chr1 4664000 4669000 Sox17 810.000000000000 181000 1.200000000000
+chr1 4674000 4679000 Sox17 810.000000000000 191000 1.600000000000
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_FL-E13-5_chr1_chr1_Tfap2d_aggregate.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_FL-E13-5_chr1_chr1_Tfap2d_aggregate.txt Wed Oct 18 10:42:59 2023 +0000
@@ -0,0 +1,10 @@
+# Chromosome Start End Gene Sum of interactions Relative position Raw
+chr1 19078000 19081000 Tfap2d 472.000000000000 -13000 0.000000000000
+chr1 19086000 19091000 Tfap2d 472.000000000000 -3000 32.800000000000
+chr1 19104000 19106000 Tfap2d 472.000000000000 12000 10.600000000000
+chr1 19109000 19114000 Tfap2d 472.000000000000 20000 18.600000000000
+chr1 19125000 19129000 Tfap2d 472.000000000000 35000 7.800000000000
+chr1 19133000 19139000 Tfap2d 472.000000000000 45000 10.000000000000
+chr1 19182000 19185000 Tfap2d 472.000000000000 91000 1.000000000000
+chr1 19189000 19238000 Tfap2d 472.000000000000 144000 25.800000000000
+chr1 19254000 19261000 Tfap2d 472.000000000000 167000 6.400000000000
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_MB-E10-5_chr1_chr1_Eya1_aggregate.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_MB-E10-5_chr1_chr1_Eya1_aggregate.txt Wed Oct 18 10:42:59 2023 +0000
@@ -0,0 +1,9 @@
+# Chromosome Start End Gene Sum of interactions Relative position Raw
+chr1 14274000 14278000 Eya1 832.000000000000 -23000 0.000000000000
+chr1 14295000 14298000 Eya1 832.000000000000 -3000 49.800000000000
+chr1 14314000 14319000 Eya1 832.000000000000 18000 23.400000000000
+chr1 14426000 14432000 Eya1 832.000000000000 131000 9.000000000000
+chr1 14447000 14455000 Eya1 832.000000000000 154000 12.400000000000
+chr1 14460000 14465000 Eya1 832.000000000000 164000 7.600000000000
+chr1 14480000 14488000 Eya1 832.000000000000 187000 3.200000000000
+chr1 14491000 14501000 Eya1 832.000000000000 200000 18.750000000000
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_MB-E10-5_chr1_chr1_Sox17_aggregate.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_MB-E10-5_chr1_chr1_Sox17_aggregate.txt Wed Oct 18 10:42:59 2023 +0000
@@ -0,0 +1,9 @@
+# Chromosome Start End Gene Sum of interactions Relative position Raw
+chr1 4481000 4488000 Sox17 978.000000000000 0 400.400000000000
+chr1 4499000 4502000 Sox17 978.000000000000 14000 21.000000000000
+chr1 4509000 4515000 Sox17 978.000000000000 27000 13.200000000000
+chr1 4561000 4567000 Sox17 978.000000000000 79000 12.400000000000
+chr1 4585000 4590000 Sox17 978.000000000000 102000 2.400000000000
+chr1 4652000 4658000 Sox17 978.000000000000 170000 5.000000000000
+chr1 4664000 4669000 Sox17 978.000000000000 181000 5.400000000000
+chr1 4674000 4679000 Sox17 978.000000000000 191000 5.200000000000
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_MB-E10-5_chr1_chr1_Tfap2d_aggregate.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/aggregate/FL-E13-5_chr1_MB-E10-5_chr1_MB-E10-5_chr1_chr1_Tfap2d_aggregate.txt Wed Oct 18 10:42:59 2023 +0000
@@ -0,0 +1,10 @@
+# Chromosome Start End Gene Sum of interactions Relative position Raw
+chr1 19078000 19081000 Tfap2d 800.000000000000 -13000 9.000000000000
+chr1 19086000 19091000 Tfap2d 800.000000000000 -3000 88.600000000000
+chr1 19104000 19106000 Tfap2d 800.000000000000 12000 14.800000000000
+chr1 19109000 19114000 Tfap2d 800.000000000000 20000 22.200000000000
+chr1 19125000 19129000 Tfap2d 800.000000000000 35000 8.800000000000
+chr1 19133000 19139000 Tfap2d 800.000000000000 45000 12.800000000000
+chr1 19182000 19185000 Tfap2d 800.000000000000 91000 5.000000000000
+chr1 19189000 19238000 Tfap2d 800.000000000000 144000 126.600000000000
+chr1 19254000 19261000 Tfap2d 800.000000000000 167000 1.400000000000
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/cHi-C/chicAggregateStatistic/aggregate.hdf5
Binary file test-data/cHi-C/chicAggregateStatistic/aggregate.hdf5 has changed
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/cHi-C/chicDifferentialTest/differential.hdf5
Binary file test-data/cHi-C/chicDifferentialTest/differential.hdf5 has changed
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/cHi-C/chicExportData/aggregate.tar.gz
Binary file test-data/cHi-C/chicExportData/aggregate.tar.gz has changed
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/cHi-C/chicExportData/oneGene/FL-E13-5_chr1_genes_Eya1.bigwig
Binary file test-data/cHi-C/chicExportData/oneGene/FL-E13-5_chr1_genes_Eya1.bigwig has changed
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/cHi-C/chicExportData/oneGene/FL-E13-5_chr1_genes_Eya1_interactions.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicExportData/oneGene/FL-E13-5_chr1_genes_Eya1_interactions.txt Wed Oct 18 10:42:59 2023 +0000
@@ -0,0 +1,402 @@
+# Chromosome Start End Gene Sum of interactions Relative position Relative Interactions p-value x-fold Raw
+chr1 14100000 14101000 Eya1 673.000000000000 -200000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14101000 14102000 Eya1 673.000000000000 -199000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14102000 14103000 Eya1 673.000000000000 -198000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14103000 14104000 Eya1 673.000000000000 -197000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14104000 14105000 Eya1 673.000000000000 -196000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14105000 14106000 Eya1 673.000000000000 -195000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14106000 14107000 Eya1 673.000000000000 -194000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14107000 14108000 Eya1 673.000000000000 -193000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14108000 14109000 Eya1 673.000000000000 -192000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14109000 14110000 Eya1 673.000000000000 -191000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14110000 14111000 Eya1 673.000000000000 -190000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14111000 14112000 Eya1 673.000000000000 -189000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14112000 14113000 Eya1 673.000000000000 -188000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14113000 14114000 Eya1 673.000000000000 -187000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14114000 14115000 Eya1 673.000000000000 -186000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14115000 14116000 Eya1 673.000000000000 -185000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14116000 14117000 Eya1 673.000000000000 -184000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14117000 14118000 Eya1 673.000000000000 -183000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14118000 14119000 Eya1 673.000000000000 -182000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14119000 14120000 Eya1 673.000000000000 -181000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14120000 14121000 Eya1 673.000000000000 -180000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14121000 14122000 Eya1 673.000000000000 -179000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14122000 14123000 Eya1 673.000000000000 -178000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14123000 14124000 Eya1 673.000000000000 -177000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14124000 14125000 Eya1 673.000000000000 -176000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14125000 14126000 Eya1 673.000000000000 -175000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14126000 14127000 Eya1 673.000000000000 -174000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14127000 14128000 Eya1 673.000000000000 -173000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14128000 14129000 Eya1 673.000000000000 -172000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14129000 14130000 Eya1 673.000000000000 -171000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14130000 14131000 Eya1 673.000000000000 -170000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14131000 14132000 Eya1 673.000000000000 -169000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14132000 14133000 Eya1 673.000000000000 -168000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14133000 14134000 Eya1 673.000000000000 -167000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14134000 14135000 Eya1 673.000000000000 -166000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14135000 14136000 Eya1 673.000000000000 -165000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14136000 14137000 Eya1 673.000000000000 -164000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14137000 14138000 Eya1 673.000000000000 -163000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14138000 14139000 Eya1 673.000000000000 -162000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14139000 14140000 Eya1 673.000000000000 -161000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14140000 14141000 Eya1 673.000000000000 -160000 0.000891530461 0.012107544045 4.242405017910 0.600000000000
+chr1 14141000 14142000 Eya1 673.000000000000 -159000 0.000891530461 0.012107544045 4.789812097144 0.600000000000
+chr1 14142000 14143000 Eya1 673.000000000000 -158000 0.000891530461 0.012107544045 4.303889149198 0.600000000000
+chr1 14143000 14144000 Eya1 673.000000000000 -157000 0.000891530461 0.012107544045 4.367181637306 0.600000000000
+chr1 14144000 14145000 Eya1 673.000000000000 -156000 0.000891530461 0.012107544045 5.120143967809 0.600000000000
+chr1 14145000 14146000 Eya1 673.000000000000 -155000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14146000 14147000 Eya1 673.000000000000 -154000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14147000 14148000 Eya1 673.000000000000 -153000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14148000 14149000 Eya1 673.000000000000 -152000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14149000 14150000 Eya1 673.000000000000 -151000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14150000 14151000 Eya1 673.000000000000 -150000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14151000 14152000 Eya1 673.000000000000 -149000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14152000 14153000 Eya1 673.000000000000 -148000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14153000 14154000 Eya1 673.000000000000 -147000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14154000 14155000 Eya1 673.000000000000 -146000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14155000 14156000 Eya1 673.000000000000 -145000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14156000 14157000 Eya1 673.000000000000 -144000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14157000 14158000 Eya1 673.000000000000 -143000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14158000 14159000 Eya1 673.000000000000 -142000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14159000 14160000 Eya1 673.000000000000 -141000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14160000 14161000 Eya1 673.000000000000 -140000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14161000 14162000 Eya1 673.000000000000 -139000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14162000 14163000 Eya1 673.000000000000 -138000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14163000 14164000 Eya1 673.000000000000 -137000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14164000 14165000 Eya1 673.000000000000 -136000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14165000 14166000 Eya1 673.000000000000 -135000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14166000 14167000 Eya1 673.000000000000 -134000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14167000 14168000 Eya1 673.000000000000 -133000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14168000 14169000 Eya1 673.000000000000 -132000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14169000 14170000 Eya1 673.000000000000 -131000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14170000 14171000 Eya1 673.000000000000 -130000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14171000 14172000 Eya1 673.000000000000 -129000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14172000 14173000 Eya1 673.000000000000 -128000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14173000 14174000 Eya1 673.000000000000 -127000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14174000 14175000 Eya1 673.000000000000 -126000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14175000 14176000 Eya1 673.000000000000 -125000 0.000297176820 0.042850447268 0.916568982282 0.200000000000
+chr1 14176000 14177000 Eya1 673.000000000000 -124000 0.000297176820 0.042850447268 0.908160092485 0.200000000000
+chr1 14177000 14178000 Eya1 673.000000000000 -123000 0.000297176820 0.042850447268 0.798302018335 0.200000000000
+chr1 14178000 14179000 Eya1 673.000000000000 -122000 0.000297176820 0.042850447268 0.925135047590 0.200000000000
+chr1 14179000 14180000 Eya1 673.000000000000 -121000 0.000297176820 0.042850447268 0.883834378206 0.200000000000
+chr1 14180000 14181000 Eya1 673.000000000000 -120000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14181000 14182000 Eya1 673.000000000000 -119000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14182000 14183000 Eya1 673.000000000000 -118000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14183000 14184000 Eya1 673.000000000000 -117000 0.000297176820 0.042850447268 0.860777829009 0.200000000000
+chr1 14184000 14185000 Eya1 673.000000000000 -116000 0.000297176820 0.042850447268 0.791915602137 0.200000000000
+chr1 14185000 14186000 Eya1 673.000000000000 -115000 0.000297176820 0.042850447268 0.761457309513 0.200000000000
+chr1 14186000 14187000 Eya1 673.000000000000 -114000 0.000297176820 0.042850447268 0.811388936776 0.200000000000
+chr1 14187000 14188000 Eya1 673.000000000000 -113000 0.000297176820 0.042850447268 0.891796850153 0.200000000000
+chr1 14188000 14189000 Eya1 673.000000000000 -112000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14189000 14190000 Eya1 673.000000000000 -111000 0.000297176820 0.042850447268 1.064402690160 0.200000000000
+chr1 14190000 14191000 Eya1 673.000000000000 -110000 0.000297176820 0.042850447268 1.207188418049 0.200000000000
+chr1 14191000 14192000 Eya1 673.000000000000 -109000 0.000297176820 0.042850447268 1.010096430089 0.200000000000
+chr1 14192000 14193000 Eya1 673.000000000000 -108000 0.000297176820 0.042850447268 0.951821635672 0.200000000000
+chr1 14193000 14194000 Eya1 673.000000000000 -107000 0.000297176820 0.042850447268 0.824912085835 0.200000000000
+chr1 14194000 14195000 Eya1 673.000000000000 -106000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14195000 14196000 Eya1 673.000000000000 -105000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14196000 14197000 Eya1 673.000000000000 -104000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14197000 14198000 Eya1 673.000000000000 -103000 0.001188707281 0.006261619191 5.424079472832 0.800000000000
+chr1 14198000 14199000 Eya1 673.000000000000 -102000 0.001188707281 0.006261619191 5.499413910652 0.800000000000
+chr1 14199000 14200000 Eya1 673.000000000000 -101000 0.001188707281 0.006261619191 5.822908849742 0.800000000000
+chr1 14200000 14201000 Eya1 673.000000000000 -100000 0.001188707281 0.006261619191 4.888367915554 0.800000000000
+chr1 14201000 14202000 Eya1 673.000000000000 -99000 0.001188707281 0.006261619191 4.499520464782 0.800000000000
+chr1 14202000 14203000 Eya1 673.000000000000 -98000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14203000 14204000 Eya1 673.000000000000 -97000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14204000 14205000 Eya1 673.000000000000 -96000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14205000 14206000 Eya1 673.000000000000 -95000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14206000 14207000 Eya1 673.000000000000 -94000 0.000594353640 0.023000625561 1.546710160135 0.400000000000
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+chr1 14403000 14404000 Eya1 673.000000000000 103000 0.000297176820 0.000000000000 0.324555574533 0.200000000000
+chr1 14404000 14405000 Eya1 673.000000000000 104000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14405000 14406000 Eya1 673.000000000000 105000 0.000594353640 0.000000000000 0.592751199195 0.400000000000
+chr1 14406000 14407000 Eya1 673.000000000000 106000 0.000594353640 0.000000000000 0.578885673960 0.400000000000
+chr1 14407000 14408000 Eya1 673.000000000000 107000 0.000594353640 0.000000000000 0.556120506836 0.400000000000
+chr1 14408000 14409000 Eya1 673.000000000000 108000 0.000891530461 0.000000000000 0.813611919440 0.600000000000
+chr1 14409000 14410000 Eya1 673.000000000000 109000 0.000891530461 0.000000000000 0.843660087147 0.600000000000
+chr1 14410000 14411000 Eya1 673.000000000000 110000 0.000297176820 0.000000000000 0.291145441917 0.200000000000
+chr1 14411000 14412000 Eya1 673.000000000000 111000 0.000297176820 0.000000000000 0.275736630113 0.200000000000
+chr1 14412000 14413000 Eya1 673.000000000000 112000 0.000297176820 0.000000000000 0.282827000656 0.200000000000
+chr1 14413000 14414000 Eya1 673.000000000000 113000 0.000297176820 0.000000000000 0.290291642960 0.200000000000
+chr1 14414000 14415000 Eya1 673.000000000000 114000 0.000297176820 0.000000000000 0.286096676989 0.200000000000
+chr1 14415000 14416000 Eya1 673.000000000000 115000 0.000297176820 0.000000000000 0.288598980306 0.200000000000
+chr1 14416000 14417000 Eya1 673.000000000000 116000 0.000594353640 0.000000000000 0.664358726512 0.400000000000
+chr1 14417000 14418000 Eya1 673.000000000000 117000 0.000891530461 0.000000000000 1.017014899996 0.600000000000
+chr1 14418000 14419000 Eya1 673.000000000000 118000 0.000594353640 0.000000000000 0.687426738036 0.400000000000
+chr1 14419000 14420000 Eya1 673.000000000000 119000 0.000594353640 0.000000000000 0.671114917005 0.400000000000
+chr1 14420000 14421000 Eya1 673.000000000000 120000 0.000594353640 0.000000000000 0.662136790955 0.400000000000
+chr1 14421000 14422000 Eya1 673.000000000000 121000 0.000297176820 0.000000000000 0.325623191563 0.200000000000
+chr1 14422000 14423000 Eya1 673.000000000000 122000 0.000594353640 0.000000000000 0.668847636862 0.400000000000
+chr1 14423000 14424000 Eya1 673.000000000000 123000 0.000594353640 0.000000000000 0.682685863943 0.400000000000
+chr1 14424000 14425000 Eya1 673.000000000000 124000 0.000594353640 0.000000000000 0.725197437366 0.400000000000
+chr1 14425000 14426000 Eya1 673.000000000000 125000 0.000594353640 0.000000000000 0.791915602137 0.400000000000
+chr1 14426000 14427000 Eya1 673.000000000000 126000 0.001188707281 0.000000000000 1.477454480806 0.800000000000
+chr1 14427000 14428000 Eya1 673.000000000000 127000 0.000594353640 0.000000000000 0.755644658251 0.400000000000
+chr1 14428000 14429000 Eya1 673.000000000000 128000 0.000594353640 0.000000000000 0.791915602137 0.400000000000
+chr1 14429000 14430000 Eya1 673.000000000000 129000 0.000594353640 0.000000000000 0.764397299148 0.400000000000
+chr1 14430000 14431000 Eya1 673.000000000000 130000 0.000594353640 0.000000000000 0.714725272130 0.400000000000
+chr1 14431000 14432000 Eya1 673.000000000000 131000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14432000 14433000 Eya1 673.000000000000 132000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14433000 14434000 Eya1 673.000000000000 133000 0.000297176820 0.000000000000 0.358657428234 0.200000000000
+chr1 14434000 14435000 Eya1 673.000000000000 134000 0.000297176820 0.000000000000 0.373545095179 0.200000000000
+chr1 14435000 14436000 Eya1 673.000000000000 135000 0.000297176820 0.000000000000 0.391262649240 0.200000000000
+chr1 14436000 14437000 Eya1 673.000000000000 136000 0.000297176820 0.000000000000 0.358657428234 0.200000000000
+chr1 14437000 14438000 Eya1 673.000000000000 137000 0.000297176820 0.000000000000 0.334423818431 0.200000000000
+chr1 14438000 14439000 Eya1 673.000000000000 138000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14439000 14440000 Eya1 673.000000000000 139000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14440000 14441000 Eya1 673.000000000000 140000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14441000 14442000 Eya1 673.000000000000 141000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14442000 14443000 Eya1 673.000000000000 142000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14443000 14444000 Eya1 673.000000000000 143000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14444000 14445000 Eya1 673.000000000000 144000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14445000 14446000 Eya1 673.000000000000 145000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14446000 14447000 Eya1 673.000000000000 146000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14447000 14448000 Eya1 673.000000000000 147000 0.000594353640 0.000000000000 0.868328510517 0.400000000000
+chr1 14448000 14449000 Eya1 673.000000000000 148000 0.000594353640 0.000000000000 0.899904092956 0.400000000000
+chr1 14449000 14450000 Eya1 673.000000000000 149000 0.000891530461 0.000000000000 1.387702573545 0.600000000000
+chr1 14450000 14451000 Eya1 673.000000000000 150000 0.001188707281 0.000000000000 1.721555655524 0.800000000000
+chr1 14451000 14452000 Eya1 673.000000000000 151000 0.001188707281 0.000000000000 1.816320187745 0.800000000000
+chr1 14452000 14453000 Eya1 673.000000000000 152000 0.000594353640 0.000000000000 0.879906224076 0.400000000000
+chr1 14453000 14454000 Eya1 673.000000000000 153000 0.000594353640 0.000000000000 0.887797759777 0.400000000000
+chr1 14454000 14455000 Eya1 673.000000000000 154000 0.000891530461 0.000000000000 1.356019866146 0.600000000000
+chr1 14455000 14456000 Eya1 673.000000000000 155000 0.000594353640 0.000000000000 0.876012833675 0.400000000000
+chr1 14456000 14457000 Eya1 673.000000000000 156000 0.000594353640 0.000000000000 0.876012833675 0.400000000000
+chr1 14457000 14458000 Eya1 673.000000000000 157000 0.000594353640 0.000000000000 0.821489212945 0.400000000000
+chr1 14458000 14459000 Eya1 673.000000000000 158000 0.001188707281 0.000000000000 1.583831204275 0.800000000000
+chr1 14459000 14460000 Eya1 673.000000000000 159000 0.000594353640 0.000000000000 0.770345916308 0.400000000000
+chr1 14460000 14461000 Eya1 673.000000000000 160000 0.001188707281 0.000000000000 1.517079697070 0.800000000000
+chr1 14461000 14462000 Eya1 673.000000000000 161000 0.001188707281 0.000000000000 1.429450544260 0.800000000000
+chr1 14462000 14463000 Eya1 673.000000000000 162000 0.001188707281 0.000000000000 1.616154290340 0.800000000000
+chr1 14463000 14464000 Eya1 673.000000000000 163000 0.000594353640 0.000000000000 0.821489212945 0.400000000000
+chr1 14464000 14465000 Eya1 673.000000000000 164000 0.000594353640 0.000000000000 0.857051516792 0.400000000000
+chr1 14465000 14466000 Eya1 673.000000000000 165000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14466000 14467000 Eya1 673.000000000000 166000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14467000 14468000 Eya1 673.000000000000 167000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14468000 14469000 Eya1 673.000000000000 168000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14469000 14470000 Eya1 673.000000000000 169000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14470000 14471000 Eya1 673.000000000000 170000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14471000 14472000 Eya1 673.000000000000 171000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14472000 14473000 Eya1 673.000000000000 172000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14473000 14474000 Eya1 673.000000000000 173000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14474000 14475000 Eya1 673.000000000000 174000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14475000 14476000 Eya1 673.000000000000 175000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14476000 14477000 Eya1 673.000000000000 176000 0.000297176820 0.000000000000 0.421231702882 0.200000000000
+chr1 14477000 14478000 Eya1 673.000000000000 177000 0.000297176820 0.000000000000 0.449952046478 0.200000000000
+chr1 14478000 14479000 Eya1 673.000000000000 178000 0.000594353640 0.000000000000 0.933862738240 0.400000000000
+chr1 14479000 14480000 Eya1 673.000000000000 179000 0.000594353640 0.000000000000 0.951821637197 0.400000000000
+chr1 14480000 14481000 Eya1 673.000000000000 180000 0.001485884101 0.000000000000 2.512422592521 1.000000000000
+chr1 14481000 14482000 Eya1 673.000000000000 181000 0.001188707281 0.000000000000 2.020192860178 0.800000000000
+chr1 14482000 14483000 Eya1 673.000000000000 182000 0.001188707281 0.000000000000 2.128805380321 0.800000000000
+chr1 14483000 14484000 Eya1 673.000000000000 183000 0.001783060921 0.000000000000 3.093420317586 1.200000000000
+chr1 14484000 14485000 Eya1 673.000000000000 184000 0.002080237741 0.000000000000 3.380127570538 1.400000000000
+chr1 14485000 14486000 Eya1 673.000000000000 185000 0.001188707281 0.000000000000 1.903643274393 0.800000000000
+chr1 14486000 14487000 Eya1 673.000000000000 186000 0.001188707281 0.000000000000 2.106158514412 0.800000000000
+chr1 14487000 14488000 Eya1 673.000000000000 187000 0.001188707281 0.000000000000 2.140312436513 0.800000000000
+chr1 14488000 14489000 Eya1 673.000000000000 188000 0.000594353640 0.000000000000 1.058710697124 0.400000000000
+chr1 14489000 14490000 Eya1 673.000000000000 189000 0.000297176820 0.000000000000 0.575520059550 0.200000000000
+chr1 14490000 14491000 Eya1 673.000000000000 190000 0.000297176820 0.000000000000 0.578885673960 0.200000000000
+chr1 14491000 14492000 Eya1 673.000000000000 191000 0.002080237741 0.000000000000 3.849589730333 1.400000000000
+chr1 14492000 14493000 Eya1 673.000000000000 192000 0.003268945022 0.000000000000 5.982878858272 2.200000000000
+chr1 14493000 14494000 Eya1 673.000000000000 193000 0.002971768202 0.000000000000 5.892229182196 2.000000000000
+chr1 14494000 14495000 Eya1 673.000000000000 194000 0.003268945022 0.000000000000 6.294126893758 2.200000000000
+chr1 14495000 14496000 Eya1 673.000000000000 195000 0.003268945022 0.000000000000 6.680269651133 2.200000000000
+chr1 14496000 14497000 Eya1 673.000000000000 196000 0.002971768202 0.000000000000 6.072972410121 2.000000000000
+chr1 14497000 14498000 Eya1 673.000000000000 197000 0.002080237741 0.000000000000 3.937080406684 1.400000000000
+chr1 14498000 14499000 Eya1 673.000000000000 198000 0.002971768202 0.000000000000 4.852424033528 2.000000000000
+chr1 14499000 14500000 Eya1 673.000000000000 199000 0.003343239227 0.000000000000 5.830530441735 2.250000000000
+chr1 14500000 14501000 Eya1 673.000000000000 200000 0.004457652303 0.000000000000 7.575723225668 3.000000000000
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/cHi-C/chicExportData/oneGene/MB-E10-5_chr1_genes_Eya1.bigwig
Binary file test-data/cHi-C/chicExportData/oneGene/MB-E10-5_chr1_genes_Eya1.bigwig has changed
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/cHi-C/chicExportData/oneGene/MB-E10-5_chr1_genes_Eya1_interactions.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/chicExportData/oneGene/MB-E10-5_chr1_genes_Eya1_interactions.txt Wed Oct 18 10:42:59 2023 +0000
@@ -0,0 +1,402 @@
+# Chromosome Start End Gene Sum of interactions Relative position Relative Interactions p-value x-fold Raw
+chr1 14100000 14101000 Eya1 832.000000000000 -200000 0.000400641026 0.028365821799 2.426424093120 0.333333333333
+chr1 14101000 14102000 Eya1 832.000000000000 -199000 0.000300480769 0.036748857670 1.429857059822 0.250000000000
+chr1 14102000 14103000 Eya1 832.000000000000 -198000 0.000240384615 0.042850447268 0.931069711724 0.200000000000
+chr1 14103000 14104000 Eya1 832.000000000000 -197000 0.000240384615 0.042850447268 0.889688835341 0.200000000000
+chr1 14104000 14105000 Eya1 832.000000000000 -196000 0.000240384615 0.042850447268 0.976487746811 0.200000000000
+chr1 14105000 14106000 Eya1 832.000000000000 -195000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14106000 14107000 Eya1 832.000000000000 -194000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14107000 14108000 Eya1 832.000000000000 -193000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14108000 14109000 Eya1 832.000000000000 -192000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14109000 14110000 Eya1 832.000000000000 -191000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14110000 14111000 Eya1 832.000000000000 -190000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14111000 14112000 Eya1 832.000000000000 -189000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14112000 14113000 Eya1 832.000000000000 -188000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14113000 14114000 Eya1 832.000000000000 -187000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14114000 14115000 Eya1 832.000000000000 -186000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14115000 14116000 Eya1 832.000000000000 -185000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14116000 14117000 Eya1 832.000000000000 -184000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14117000 14118000 Eya1 832.000000000000 -183000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14118000 14119000 Eya1 832.000000000000 -182000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14119000 14120000 Eya1 832.000000000000 -181000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14120000 14121000 Eya1 832.000000000000 -180000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14121000 14122000 Eya1 832.000000000000 -179000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14122000 14123000 Eya1 832.000000000000 -178000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14123000 14124000 Eya1 832.000000000000 -177000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14124000 14125000 Eya1 832.000000000000 -176000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14125000 14126000 Eya1 832.000000000000 -175000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14126000 14127000 Eya1 832.000000000000 -174000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14127000 14128000 Eya1 832.000000000000 -173000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14128000 14129000 Eya1 832.000000000000 -172000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14129000 14130000 Eya1 832.000000000000 -171000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14130000 14131000 Eya1 832.000000000000 -170000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14131000 14132000 Eya1 832.000000000000 -169000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14132000 14133000 Eya1 832.000000000000 -168000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14133000 14134000 Eya1 832.000000000000 -167000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14134000 14135000 Eya1 832.000000000000 -166000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14135000 14136000 Eya1 832.000000000000 -165000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14136000 14137000 Eya1 832.000000000000 -164000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14137000 14138000 Eya1 832.000000000000 -163000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14138000 14139000 Eya1 832.000000000000 -162000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14139000 14140000 Eya1 832.000000000000 -161000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14140000 14141000 Eya1 832.000000000000 -160000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14141000 14142000 Eya1 832.000000000000 -159000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14142000 14143000 Eya1 832.000000000000 -158000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14143000 14144000 Eya1 832.000000000000 -157000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14144000 14145000 Eya1 832.000000000000 -156000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14145000 14146000 Eya1 832.000000000000 -155000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14146000 14147000 Eya1 832.000000000000 -154000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14147000 14148000 Eya1 832.000000000000 -153000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14148000 14149000 Eya1 832.000000000000 -152000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14149000 14150000 Eya1 832.000000000000 -151000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14150000 14151000 Eya1 832.000000000000 -150000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14151000 14152000 Eya1 832.000000000000 -149000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14152000 14153000 Eya1 832.000000000000 -148000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14153000 14154000 Eya1 832.000000000000 -147000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14154000 14155000 Eya1 832.000000000000 -146000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14155000 14156000 Eya1 832.000000000000 -145000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14156000 14157000 Eya1 832.000000000000 -144000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14157000 14158000 Eya1 832.000000000000 -143000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14158000 14159000 Eya1 832.000000000000 -142000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14159000 14160000 Eya1 832.000000000000 -141000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14160000 14161000 Eya1 832.000000000000 -140000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14161000 14162000 Eya1 832.000000000000 -139000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14162000 14163000 Eya1 832.000000000000 -138000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14163000 14164000 Eya1 832.000000000000 -137000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14164000 14165000 Eya1 832.000000000000 -136000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14165000 14166000 Eya1 832.000000000000 -135000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14166000 14167000 Eya1 832.000000000000 -134000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14167000 14168000 Eya1 832.000000000000 -133000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14168000 14169000 Eya1 832.000000000000 -132000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14169000 14170000 Eya1 832.000000000000 -131000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14170000 14171000 Eya1 832.000000000000 -130000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14171000 14172000 Eya1 832.000000000000 -129000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14172000 14173000 Eya1 832.000000000000 -128000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14173000 14174000 Eya1 832.000000000000 -127000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14174000 14175000 Eya1 832.000000000000 -126000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14175000 14176000 Eya1 832.000000000000 -125000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14176000 14177000 Eya1 832.000000000000 -124000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14177000 14178000 Eya1 832.000000000000 -123000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14178000 14179000 Eya1 832.000000000000 -122000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14179000 14180000 Eya1 832.000000000000 -121000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14180000 14181000 Eya1 832.000000000000 -120000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14181000 14182000 Eya1 832.000000000000 -119000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14182000 14183000 Eya1 832.000000000000 -118000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14183000 14184000 Eya1 832.000000000000 -117000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14184000 14185000 Eya1 832.000000000000 -116000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14185000 14186000 Eya1 832.000000000000 -115000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14186000 14187000 Eya1 832.000000000000 -114000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14187000 14188000 Eya1 832.000000000000 -113000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14188000 14189000 Eya1 832.000000000000 -112000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14189000 14190000 Eya1 832.000000000000 -111000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14190000 14191000 Eya1 832.000000000000 -110000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14191000 14192000 Eya1 832.000000000000 -109000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14192000 14193000 Eya1 832.000000000000 -108000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
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+chr1 14390000 14391000 Eya1 832.000000000000 90000 0.001201923077 0.000000000000 0.983685444445 1.000000000000
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+chr1 14392000 14393000 Eya1 832.000000000000 92000 0.000721153846 0.000000000000 0.635492025580 0.600000000000
+chr1 14393000 14394000 Eya1 832.000000000000 93000 0.000961538462 0.000000000000 0.879912034881 0.800000000000
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+chr1 14397000 14398000 Eya1 832.000000000000 97000 0.000721153846 0.000000000000 0.584467118044 0.600000000000
+chr1 14398000 14399000 Eya1 832.000000000000 98000 0.000480769231 0.000000000000 0.380389525993 0.400000000000
+chr1 14399000 14400000 Eya1 832.000000000000 99000 0.000240384615 0.000000000000 0.204265293878 0.200000000000
+chr1 14400000 14401000 Eya1 832.000000000000 100000 0.000721153846 0.000000000000 0.684376027315 0.600000000000
+chr1 14401000 14402000 Eya1 832.000000000000 101000 0.000480769231 0.000000000000 0.488243872910 0.400000000000
+chr1 14402000 14403000 Eya1 832.000000000000 102000 0.000721153846 0.000000000000 0.712807079120 0.600000000000
+chr1 14403000 14404000 Eya1 832.000000000000 103000 0.000721153846 0.000000000000 0.787593395411 0.600000000000
+chr1 14404000 14405000 Eya1 832.000000000000 104000 0.000961538462 0.000000000000 1.000899939643 0.800000000000
+chr1 14405000 14406000 Eya1 832.000000000000 105000 0.000961538462 0.000000000000 0.958946050621 0.800000000000
+chr1 14406000 14407000 Eya1 832.000000000000 106000 0.001201923077 0.000000000000 1.170643204852 1.000000000000
+chr1 14407000 14408000 Eya1 832.000000000000 107000 0.000961538462 0.000000000000 0.899685339184 0.800000000000
+chr1 14408000 14409000 Eya1 832.000000000000 108000 0.001201923077 0.000000000000 1.096876646200 1.000000000000
+chr1 14409000 14410000 Eya1 832.000000000000 109000 0.000961538462 0.000000000000 0.909909036298 0.800000000000
+chr1 14410000 14411000 Eya1 832.000000000000 110000 0.000480769231 0.000000000000 0.471011736562 0.400000000000
+chr1 14411000 14412000 Eya1 832.000000000000 111000 0.000480769231 0.000000000000 0.446083538620 0.400000000000
+chr1 14412000 14413000 Eya1 832.000000000000 112000 0.000480769231 0.000000000000 0.457554258272 0.400000000000
+chr1 14413000 14414000 Eya1 832.000000000000 113000 0.000240384615 0.000000000000 0.234815235231 0.200000000000
+chr1 14414000 14415000 Eya1 832.000000000000 114000 0.000480769231 0.000000000000 0.462843902917 0.400000000000
+chr1 14415000 14416000 Eya1 832.000000000000 115000 0.000480769231 0.000000000000 0.466892100350 0.400000000000
+chr1 14416000 14417000 Eya1 832.000000000000 116000 0.000240384615 0.000000000000 0.268697970519 0.200000000000
+chr1 14417000 14418000 Eya1 832.000000000000 117000 0.000240384615 0.000000000000 0.274219161738 0.200000000000
+chr1 14418000 14419000 Eya1 832.000000000000 118000 0.000480769231 0.000000000000 0.556055522474 0.400000000000
+chr1 14419000 14420000 Eya1 832.000000000000 119000 0.000240384615 0.000000000000 0.271430492274 0.200000000000
+chr1 14420000 14421000 Eya1 832.000000000000 120000 0.000480769231 0.000000000000 0.535598630183 0.400000000000
+chr1 14421000 14422000 Eya1 832.000000000000 121000 0.000480769231 0.000000000000 0.526789442119 0.400000000000
+chr1 14422000 14423000 Eya1 832.000000000000 122000 0.000480769231 0.000000000000 0.541026994721 0.400000000000
+chr1 14423000 14424000 Eya1 832.000000000000 123000 0.000240384615 0.000000000000 0.276110328386 0.200000000000
+chr1 14424000 14425000 Eya1 832.000000000000 124000 0.000480769231 0.000000000000 0.586608023254 0.400000000000
+chr1 14425000 14426000 Eya1 832.000000000000 125000 0.000240384615 0.000000000000 0.320287980913 0.200000000000
+chr1 14426000 14427000 Eya1 832.000000000000 126000 0.001682692308 0.000000000000 2.091432710060 1.400000000000
+chr1 14427000 14428000 Eya1 832.000000000000 127000 0.001923076923 0.000000000000 2.444946418284 1.600000000000
+chr1 14428000 14429000 Eya1 832.000000000000 128000 0.001923076923 0.000000000000 2.562303847300 1.600000000000
+chr1 14429000 14430000 Eya1 832.000000000000 129000 0.001682692308 0.000000000000 2.164107978537 1.400000000000
+chr1 14430000 14431000 Eya1 832.000000000000 130000 0.002403846154 0.000000000000 2.890685746055 2.000000000000
+chr1 14431000 14432000 Eya1 832.000000000000 131000 0.001201923077 0.000000000000 1.570039121874 1.000000000000
+chr1 14432000 14433000 Eya1 832.000000000000 132000 0.000961538462 0.000000000000 1.286297112140 0.800000000000
+chr1 14433000 14434000 Eya1 832.000000000000 133000 0.000961538462 0.000000000000 1.160463698084 0.800000000000
+chr1 14434000 14435000 Eya1 832.000000000000 134000 0.001442307692 0.000000000000 1.812950834534 1.200000000000
+chr1 14435000 14436000 Eya1 832.000000000000 135000 0.000721153846 0.000000000000 0.949470299058 0.600000000000
+chr1 14436000 14437000 Eya1 832.000000000000 136000 0.000480769231 0.000000000000 0.580231849042 0.400000000000
+chr1 14437000 14438000 Eya1 832.000000000000 137000 0.000480769231 0.000000000000 0.541026994721 0.400000000000
+chr1 14438000 14439000 Eya1 832.000000000000 138000 0.000480769231 0.000000000000 0.602045076614 0.400000000000
+chr1 14439000 14440000 Eya1 832.000000000000 139000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14440000 14441000 Eya1 832.000000000000 140000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14441000 14442000 Eya1 832.000000000000 141000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14442000 14443000 Eya1 832.000000000000 142000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14443000 14444000 Eya1 832.000000000000 143000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14444000 14445000 Eya1 832.000000000000 144000 0.000240384615 0.000000000000 0.330876012971 0.200000000000
+chr1 14445000 14446000 Eya1 832.000000000000 145000 0.000961538462 0.000000000000 1.601439905096 0.800000000000
+chr1 14446000 14447000 Eya1 832.000000000000 146000 0.000961538462 0.000000000000 1.475981478388 0.800000000000
+chr1 14447000 14448000 Eya1 832.000000000000 147000 0.001442307692 0.000000000000 2.107157767708 1.200000000000
+chr1 14448000 14449000 Eya1 832.000000000000 148000 0.001682692308 0.000000000000 2.547745301633 1.400000000000
+chr1 14449000 14450000 Eya1 832.000000000000 149000 0.002163461538 0.000000000000 3.367513817293 1.800000000000
+chr1 14450000 14451000 Eya1 832.000000000000 150000 0.002163461538 0.000000000000 3.133251984828 1.800000000000
+chr1 14451000 14452000 Eya1 832.000000000000 151000 0.002163461538 0.000000000000 3.305724572467 1.800000000000
+chr1 14452000 14453000 Eya1 832.000000000000 152000 0.002163461538 0.000000000000 3.202879807229 1.800000000000
+chr1 14453000 14454000 Eya1 832.000000000000 153000 0.001923076923 0.000000000000 2.872537943893 1.600000000000
+chr1 14454000 14455000 Eya1 832.000000000000 154000 0.001201923077 0.000000000000 1.828127744223 1.000000000000
+chr1 14455000 14456000 Eya1 832.000000000000 155000 0.000480769231 0.000000000000 0.708601727240 0.400000000000
+chr1 14456000 14457000 Eya1 832.000000000000 156000 0.000721153846 0.000000000000 1.062902590860 0.600000000000
+chr1 14457000 14458000 Eya1 832.000000000000 157000 0.000240384615 0.000000000000 0.332248942495 0.200000000000
+chr1 14458000 14459000 Eya1 832.000000000000 158000 0.000721153846 0.000000000000 0.960863942738 0.600000000000
+chr1 14459000 14460000 Eya1 832.000000000000 159000 0.000721153846 0.000000000000 0.934692551098 0.600000000000
+chr1 14460000 14461000 Eya1 832.000000000000 160000 0.001682692308 0.000000000000 2.147524775510 1.400000000000
+chr1 14461000 14462000 Eya1 832.000000000000 161000 0.001923076923 0.000000000000 2.312548596844 1.600000000000
+chr1 14462000 14463000 Eya1 832.000000000000 162000 0.002163461538 0.000000000000 2.941420233350 1.800000000000
+chr1 14463000 14464000 Eya1 832.000000000000 163000 0.001682692308 0.000000000000 2.325742597467 1.400000000000
+chr1 14464000 14465000 Eya1 832.000000000000 164000 0.001682692308 0.000000000000 2.426424095919 1.400000000000
+chr1 14465000 14466000 Eya1 832.000000000000 165000 0.000721153846 0.000000000000 1.106986108791 0.600000000000
+chr1 14466000 14467000 Eya1 832.000000000000 166000 0.000240384615 0.000000000000 0.400359976274 0.200000000000
+chr1 14467000 14468000 Eya1 832.000000000000 167000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14468000 14469000 Eya1 832.000000000000 168000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14469000 14470000 Eya1 832.000000000000 169000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14470000 14471000 Eya1 832.000000000000 170000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14471000 14472000 Eya1 832.000000000000 171000 0.000480769231 0.000000000000 0.659028767461 0.400000000000
+chr1 14472000 14473000 Eya1 832.000000000000 172000 0.000480769231 0.000000000000 0.618316565296 0.400000000000
+chr1 14473000 14474000 Eya1 832.000000000000 173000 0.000480769231 0.000000000000 0.630488151323 0.400000000000
+chr1 14474000 14475000 Eya1 832.000000000000 174000 0.000480769231 0.000000000000 0.667266626197 0.400000000000
+chr1 14475000 14476000 Eya1 832.000000000000 175000 0.000480769231 0.000000000000 0.690275820369 0.400000000000
+chr1 14476000 14477000 Eya1 832.000000000000 176000 0.000240384615 0.000000000000 0.340731894279 0.200000000000
+chr1 14477000 14478000 Eya1 832.000000000000 177000 0.000480769231 0.000000000000 0.727927229038 0.400000000000
+chr1 14478000 14479000 Eya1 832.000000000000 178000 0.000480769231 0.000000000000 0.755396181293 0.400000000000
+chr1 14479000 14480000 Eya1 832.000000000000 179000 0.000480769231 0.000000000000 0.769923031050 0.400000000000
+chr1 14480000 14481000 Eya1 832.000000000000 180000 0.000480769231 0.000000000000 0.812913656138 0.400000000000
+chr1 14481000 14482000 Eya1 832.000000000000 181000 0.000240384615 0.000000000000 0.408530587410 0.200000000000
+chr1 14482000 14483000 Eya1 832.000000000000 182000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14483000 14484000 Eya1 832.000000000000 183000 0.000000000000 1.000000000000 0.000000000000 0.000000000000
+chr1 14484000 14485000 Eya1 832.000000000000 184000 0.000240384615 0.000000000000 0.390595098725 0.200000000000
+chr1 14485000 14486000 Eya1 832.000000000000 185000 0.000961538462 0.000000000000 1.539846062099 0.800000000000
+chr1 14486000 14487000 Eya1 832.000000000000 186000 0.000961538462 0.000000000000 1.703659471393 0.800000000000
+chr1 14487000 14488000 Eya1 832.000000000000 187000 0.000961538462 0.000000000000 1.731286381939 0.800000000000
+chr1 14488000 14489000 Eya1 832.000000000000 188000 0.001201923077 0.000000000000 2.140962437394 1.000000000000
+chr1 14489000 14490000 Eya1 832.000000000000 189000 0.001442307692 0.000000000000 2.793209135173 1.200000000000
+chr1 14490000 14491000 Eya1 832.000000000000 190000 0.000721153846 0.000000000000 1.404771845823 0.600000000000
+chr1 14491000 14492000 Eya1 832.000000000000 191000 0.001442307692 0.000000000000 2.669066506024 1.200000000000
+chr1 14492000 14493000 Eya1 832.000000000000 192000 0.002403846154 0.000000000000 4.399560174407 2.000000000000
+chr1 14493000 14494000 Eya1 832.000000000000 193000 0.002163461538 0.000000000000 4.289571172663 1.800000000000
+chr1 14494000 14495000 Eya1 832.000000000000 194000 0.001682692308 0.000000000000 3.239907320421 1.400000000000
+chr1 14495000 14496000 Eya1 832.000000000000 195000 0.002163461538 0.000000000000 4.421153111551 1.800000000000
+chr1 14496000 14497000 Eya1 832.000000000000 196000 0.001682692308 0.000000000000 3.438674642317 1.400000000000
+chr1 14497000 14498000 Eya1 832.000000000000 197000 0.001442307692 0.000000000000 2.729727108893 1.200000000000
+chr1 14498000 14499000 Eya1 832.000000000000 198000 0.002644230769 0.000000000000 4.317607586564 2.200000000000
+chr1 14499000 14500000 Eya1 832.000000000000 199000 0.003305288462 0.000000000000 5.764345200343 2.750000000000
+chr1 14500000 14501000 Eya1 832.000000000000 200000 0.003605769231 0.000000000000 6.127958811148 3.000000000000
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/cHi-C/chicExportData/oneGene/background_FL-E13-5_chr1_genes_Eya1_interactions.bigwig
Binary file test-data/cHi-C/chicExportData/oneGene/background_FL-E13-5_chr1_genes_Eya1_interactions.bigwig has changed
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/cHi-C/chicExportData/oneGene/background_MB-E10-5_chr1_genes_Eya1_interactions.bigwig
Binary file test-data/cHi-C/chicExportData/oneGene/background_MB-E10-5_chr1_genes_Eya1_interactions.bigwig has changed
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/cHi-C/chicQualityControl/histogram.png
Binary file test-data/cHi-C/chicQualityControl/histogram.png has changed
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter
--- a/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter Tue Jan 10 19:05:09 2023 +0000
+++ b/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_raw_filter Wed Oct 18 10:42:59 2023 +0000
@@ -1,4 +1,4 @@
-# Created with chicQualityControl version 3.6
+# Created with chicQualityControl version 3.7.2
# A sparsity of -1.0 indicates a faulty reference point e.g. no data for this reference point was in the matrix.
# Used Matrices 0_matrix.cool 1_matrix.cool
# Chromosome Start End Sparsity 0_matrix.cool Sparsity 1_matrix.cool
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report
--- a/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report Tue Jan 10 19:05:09 2023 +0000
+++ b/test-data/cHi-C/chicQualityControl/new_referencepoints.bed_report Wed Oct 18 10:42:59 2023 +0000
@@ -1,4 +1,4 @@
-# Created with chicQualityControl version 3.6
+# Created with chicQualityControl version 3.7.2
# QC report for matrices: 0_matrix.cool 1_matrix.cool
#Sparsity threshold for rejection: sparsity <= 0.05 are rejected.
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/cHi-C/chicQualityControl/sparsity.png
Binary file test-data/cHi-C/chicQualityControl/sparsity.png has changed
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/cHi-C/chicSignificantInteractions/significantInteractions_dual.hdf5
Binary file test-data/cHi-C/chicSignificantInteractions/significantInteractions_dual.hdf5 has changed
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/cHi-C/chicSignificantInteractions/significantInteractions_single.hdf5
Binary file test-data/cHi-C/chicSignificantInteractions/significantInteractions_single.hdf5 has changed
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/cHi-C/chicSignificantInteractions/targetFile_dual.hdf5
Binary file test-data/cHi-C/chicSignificantInteractions/targetFile_dual.hdf5 has changed
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/cHi-C/chicSignificantInteractions/targetFile_single.hdf5
Binary file test-data/cHi-C/chicSignificantInteractions/targetFile_single.hdf5 has changed
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/cHi-C/chicViewpoint/two_matrices.hdf5
Binary file test-data/cHi-C/chicViewpoint/two_matrices.hdf5 has changed
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/cHi-C/hg19.chrom.sizes
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/hg19.chrom.sizes Wed Oct 18 10:42:59 2023 +0000
@@ -0,0 +1,93 @@
+chr1 249250621
+chr2 243199373
+chr3 198022430
+chr4 191154276
+chr5 180915260
+chr6 171115067
+chr7 159138663
+chrX 155270560
+chr8 146364022
+chr9 141213431
+chr10 135534747
+chr11 135006516
+chr12 133851895
+chr13 115169878
+chr14 107349540
+chr15 102531392
+chr16 90354753
+chr17 81195210
+chr18 78077248
+chr20 63025520
+chrY 59373566
+chr19 59128983
+chr22 51304566
+chr21 48129895
+chr6_ssto_hap7 4928567
+chr6_mcf_hap5 4833398
+chr6_cox_hap2 4795371
+chr6_mann_hap4 4683263
+chr6_apd_hap1 4622290
+chr6_qbl_hap6 4611984
+chr6_dbb_hap3 4610396
+chr17_ctg5_hap1 1680828
+chr4_ctg9_hap1 590426
+chr1_gl000192_random 547496
+chrUn_gl000225 211173
+chr4_gl000194_random 191469
+chr4_gl000193_random 189789
+chr9_gl000200_random 187035
+chrUn_gl000222 186861
+chrUn_gl000212 186858
+chr7_gl000195_random 182896
+chrUn_gl000223 180455
+chrUn_gl000224 179693
+chrUn_gl000219 179198
+chr17_gl000205_random 174588
+chrUn_gl000215 172545
+chrUn_gl000216 172294
+chrUn_gl000217 172149
+chr9_gl000199_random 169874
+chrUn_gl000211 166566
+chrUn_gl000213 164239
+chrUn_gl000220 161802
+chrUn_gl000218 161147
+chr19_gl000209_random 159169
+chrUn_gl000221 155397
+chrUn_gl000214 137718
+chrUn_gl000228 129120
+chrUn_gl000227 128374
+chr1_gl000191_random 106433
+chr19_gl000208_random 92689
+chr9_gl000198_random 90085
+chr17_gl000204_random 81310
+chrUn_gl000233 45941
+chrUn_gl000237 45867
+chrUn_gl000230 43691
+chrUn_gl000242 43523
+chrUn_gl000243 43341
+chrUn_gl000241 42152
+chrUn_gl000236 41934
+chrUn_gl000240 41933
+chr17_gl000206_random 41001
+chrUn_gl000232 40652
+chrUn_gl000234 40531
+chr11_gl000202_random 40103
+chrUn_gl000238 39939
+chrUn_gl000244 39929
+chrUn_gl000248 39786
+chr8_gl000196_random 38914
+chrUn_gl000249 38502
+chrUn_gl000246 38154
+chr17_gl000203_random 37498
+chr8_gl000197_random 37175
+chrUn_gl000245 36651
+chrUn_gl000247 36422
+chr9_gl000201_random 36148
+chrUn_gl000235 34474
+chrUn_gl000239 33824
+chr21_gl000210_random 27682
+chrUn_gl000231 27386
+chrUn_gl000229 19913
+chrM 16571
+chrUn_gl000226 15008
+chr18_gl000207_random 4262
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/cHi-C/plots.tar.gz
Binary file test-data/cHi-C/plots.tar.gz has changed
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/cHi-C/referencePoints_chicViewpoint.bed
--- a/test-data/cHi-C/referencePoints_chicViewpoint.bed Tue Jan 10 19:05:09 2023 +0000
+++ b/test-data/cHi-C/referencePoints_chicViewpoint.bed Wed Oct 18 10:42:59 2023 +0000
@@ -1,4 +1,3 @@
chr1 4487435 4487435 Sox17
chr1 14300280 14300280 Eya1
-chr1 19093103 19093103 Tfap2d
-
+chr1 19093103 19093103 Tfap2d
\ No newline at end of file
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/cHi-C/target_list.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/cHi-C/target_list.bed Wed Oct 18 10:42:59 2023 +0000
@@ -0,0 +1,8 @@
+chr1 4480000 4549000
+chr1 4555000 4688000
+chr1 14274000 14279000
+chr1 14290000 14439000
+chr1 14444000 14467000
+chr1 14476000 14501000
+chr1 19077000 19118000
+chr1 19120000 19274000
\ No newline at end of file
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/distVsCounts.txt
--- a/test-data/distVsCounts.txt Tue Jan 10 19:05:09 2023 +0000
+++ b/test-data/distVsCounts.txt Wed Oct 18 10:42:59 2023 +0000
@@ -1,600 +1,600 @@
- Matrix Chromosome Distance Contacts
-0 small_test_matrix_h5 all 0 0.09142620133910055
-1 small_test_matrix_h5 all 5000 0.07741782506891134
-2 small_test_matrix_h5 all 10000 0.04433044715929309
-3 small_test_matrix_h5 all 15000 0.03461983446557299
-4 small_test_matrix_h5 all 20000 0.027541995607526563
-5 small_test_matrix_h5 all 25000 0.023782660332541568
-6 small_test_matrix_h5 all 30000 0.02002019841977069
-7 small_test_matrix_h5 all 35000 0.01967193628907643
-8 small_test_matrix_h5 all 40000 0.017480230691479873
-9 small_test_matrix_h5 all 45000 0.015494884606233642
-10 small_test_matrix_h5 all 50000 0.014013686402856293
-11 small_test_matrix_h5 all 55000 0.012799142755089891
-12 small_test_matrix_h5 all 60000 0.011404919302007028
-13 small_test_matrix_h5 all 65000 0.011588417540514775
-14 small_test_matrix_h5 all 70000 0.01084818501519938
-15 small_test_matrix_h5 all 75000 0.010554561717352416
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diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/hicCompartmentsPolarization/output_matrix.npz
Binary file test-data/hicCompartmentsPolarization/output_matrix.npz has changed
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/hicConvertFormat/GSM1436265_RAD21_ENCFF002EMQ.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicConvertFormat/GSM1436265_RAD21_ENCFF002EMQ.txt Wed Oct 18 10:42:59 2023 +0000
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diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/hicConvertFormat/hg19.chrom.sizes
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicConvertFormat/hg19.chrom.sizes Wed Oct 18 10:42:59 2023 +0000
@@ -0,0 +1,93 @@
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diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/hicConvertFormat/small_test_matrix_chr4.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicConvertFormat/small_test_matrix_chr4.bed Wed Oct 18 10:42:59 2023 +0000
@@ -0,0 +1,271 @@
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diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/hicConvertFormat/small_test_matrix_chr4.hicpro
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicConvertFormat/small_test_matrix_chr4.hicpro Wed Oct 18 10:42:59 2023 +0000
@@ -0,0 +1,326 @@
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diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/hicConvertFormat/small_test_matrix_chr4.homer
Binary file test-data/hicConvertFormat/small_test_matrix_chr4.homer has changed
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/hicDifferentialTAD/accepted.txt
--- a/test-data/hicDifferentialTAD/accepted.txt Tue Jan 10 19:05:09 2023 +0000
+++ b/test-data/hicDifferentialTAD/accepted.txt Wed Oct 18 10:42:59 2023 +0000
@@ -1,4 +1,4 @@
-# Created with HiCExplorer's hicDifferentialTAD version 3.6
+# Created with HiCExplorer's hicDifferentialTAD version 3.7.2
# H0 'regions are equal' H0 is accepted for all p-value greater the user given p-value threshold; i.e. regions in this file are not considered as differential.
# Accepted regions with Wilcoxon rank-sum test to p-value: 1.0 with used mode: all and modeReject: one
-# Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD
+# Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD W left-inter-TAD W right-inter-TAD W intra-TAD
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/hicDifferentialTAD/rejected.txt
--- a/test-data/hicDifferentialTAD/rejected.txt Tue Jan 10 19:05:09 2023 +0000
+++ b/test-data/hicDifferentialTAD/rejected.txt Wed Oct 18 10:42:59 2023 +0000
@@ -1,1402 +1,1406 @@
-# Created with HiCExplorer's hicDifferentialTAD version 3.6
+# Created with HiCExplorer's hicDifferentialTAD version 3.7.2
# H0 'regions are equal' H0 is rejected for all p-value smaller or equal the user given p-value threshold; i.e. regions in this file are considered as differential.
# Rejected regions with Wilcoxon rank-sum test to p-value: 1.0 with used mode: all and modeReject: one
-# Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD
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-chr3R 24205000 24345000 ID_0.01_1368 -0.0326015 . 1.0 1.0 1.0
-chr3R 24345000 24375000 ID_0.01_1369 -0.0623065 . 1.0 1.0 1.0
-chr3R 24375000 24450000 ID_0.01_1370 -0.0749395 . 1.0 1.0 1.0
-chr3R 24450000 24625000 ID_0.01_1371 -0.09836075 . 1.0 1.0 1.0
-chr3R 24625000 24745000 ID_0.01_1372 -0.03171375 . 1.0 1.0 1.0
-chr3R 24745000 24885000 ID_0.01_1373 -0.08589625 . 1.0 1.0 1.0
-chr3R 24885000 24995000 ID_0.01_1374 -0.09323725 . 1.0 1.0 1.0
-chr3R 24995000 25090000 ID_0.01_1375 -0.0589785 . 1.0 1.0 1.0
-chr3R 25090000 25165000 ID_0.01_1376 0.03674225 . 1.0 1.0 1.0
-chr3R 25165000 25330000 ID_0.01_1377 -0.0462465 . 1.0 1.0 1.0
-chr3R 25330000 25405000 ID_0.01_1378 -0.08303325 . 1.0 1.0 1.0
-chr3R 25405000 25570000 ID_0.01_1379 -0.00546225 . 1.0 1.0 1.0
-chr3R 25570000 25580000 ID_0.01_1380 -0.04654075 . 1.0 1.0 1.0
-chr3R 25580000 25730000 ID_0.01_1381 -0.01871575 . 1.0 1.0 1.0
-chr3R 25730000 25880000 ID_0.01_1382 -0.00858875 . 1.0 1.0 1.0
-chr3R 25880000 25990000 ID_0.01_1383 -0.10581625 . 1.0 1.0 1.0
-chr3R 25990000 26050000 ID_0.01_1384 -0.090403 . 1.0 1.0 1.0
-chr3R 26050000 26180000 ID_0.01_1385 -0.0935315 . 1.0 1.0 1.0
-chr3R 26180000 26275000 ID_0.01_1386 -0.11469275 . 1.0 1.0 1.0
-chr3R 26275000 26330000 ID_0.01_1387 -0.1002735 . 1.0 1.0 1.0
-chr3R 26330000 26490000 ID_0.01_1388 -0.092304 . 1.0 1.0 1.0
-chr3R 26490000 26565000 ID_0.01_1389 0.0627965 . 1.0 1.0 1.0
-chr3R 26565000 26640000 ID_0.01_1390 -0.01974475 . 1.0 1.0 1.0
-chr3R 26640000 26715000 ID_0.01_1391 -0.07430725 . 1.0 1.0 1.0
-chr3R 26715000 26870000 ID_0.01_1392 -0.049789 . 1.0 1.0 1.0
-chr3R 26870000 27045000 ID_0.01_1393 -0.0249905 . 1.0 1.0 1.0
-chr3R 27045000 27155000 ID_0.01_1394 -0.074189 . 1.0 1.0 1.0
-chr3R 27155000 27185000 ID_0.01_1395 -0.00609925 . 1.0 1.0 1.0
-chr3R 27185000 27250000 ID_0.01_1396 -0.01281025 . 1.0 1.0 1.0
-chr3R 27250000 27385000 ID_0.01_1397 -0.04990275 . 1.0 1.0 1.0
-chr3R 27385000 27420000 ID_0.01_1398 -0.041305 . 1.0 1.0 1.0
-chr3R 27420000 27570000 ID_0.01_1399 -0.0499295 . 1.0 1.0 1.0
-chr3R 27570000 27700000 ID_0.01_1400 -0.08094325 . 1.0 1.0 1.0
-chr3R 27700000 27750000 ID_0.01_1401 -0.01535 . 1.0 nan 1.0
-chr3R 27750000 27770000 ID_0.01_1402 0.01357725 . 1.0 nan 1.0
+# Chromosome start end name score strand p-value left-inter-TAD p-value right-inter-TAD p-value intra-TAD W left-inter-TAD W right-inter-TAD W intra-TAD
+chr3L 165000 260000 ID_0.01_1 -0.10316675 . nan 1.0 1.0 nan 0.0 0.0
+chr3L 260000 335000 ID_0.01_2 -0.026655 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 335000 360000 ID_0.01_3 -0.030848 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 360000 485000 ID_0.01_4 -0.0580815 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 485000 525000 ID_0.01_5 -0.07169775 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 525000 680000 ID_0.01_6 -0.1060405 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 680000 705000 ID_0.01_7 -0.0148855 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 705000 740000 ID_0.01_8 0.002784 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 740000 870000 ID_0.01_9 0.00949975 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 870000 1010000 ID_0.01_10 -0.09546975 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 1010000 1040000 ID_0.01_11 -0.05182175 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 1040000 1110000 ID_0.01_12 -0.05874875 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 1110000 1210000 ID_0.01_13 -0.048349 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 1210000 1245000 ID_0.01_14 -0.0567565 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 1245000 1300000 ID_0.01_15 -0.0641435 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 1300000 1465000 ID_0.01_16 -0.091379 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 1465000 1535000 ID_0.01_17 -0.01307225 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 1535000 1580000 ID_0.01_18 -0.08711525 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 1580000 1640000 ID_0.01_19 -0.08235875 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 1640000 1670000 ID_0.01_20 -0.0628755 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 1670000 1735000 ID_0.01_21 -0.037945 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 1735000 1815000 ID_0.01_22 -0.050313 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 1815000 1850000 ID_0.01_23 -0.01723525 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 1850000 1925000 ID_0.01_24 -0.0259975 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 1925000 2155000 ID_0.01_25 8.325e-05 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 2155000 2260000 ID_0.01_26 -0.0401965 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 2260000 2390000 ID_0.01_27 -0.07518575 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 2390000 2460000 ID_0.01_28 -0.072071 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 2460000 2560000 ID_0.01_29 -0.09132325 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 2560000 2600000 ID_0.01_30 -0.09179675 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 2600000 2740000 ID_0.01_31 -0.0934855 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 2740000 2885000 ID_0.01_32 -0.08927875 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 2885000 2945000 ID_0.01_33 -0.08972575 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 2945000 2960000 ID_0.01_34 0.029899 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 2960000 3045000 ID_0.01_35 0.0356865 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 3045000 3135000 ID_0.01_36 -0.00466875 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 3135000 3220000 ID_0.01_37 0.055702 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 3220000 3255000 ID_0.01_38 -0.059463 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 3255000 3315000 ID_0.01_39 -0.045796 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 3315000 3345000 ID_0.01_40 -0.05499875 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 3345000 3475000 ID_0.01_41 -0.04234075 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 3475000 3515000 ID_0.01_42 -0.05097675 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 3515000 3545000 ID_0.01_43 -0.012488 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 3545000 3615000 ID_0.01_44 0.02457925 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 3615000 3670000 ID_0.01_45 0.019683 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 3670000 3765000 ID_0.01_46 0.09945325 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 3765000 3785000 ID_0.01_47 -0.047454 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 3785000 3825000 ID_0.01_48 -0.041084 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 3825000 3900000 ID_0.01_49 -0.06101175 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 3900000 4000000 ID_0.01_50 -0.0684535 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 4000000 4120000 ID_0.01_51 -0.03007875 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 4120000 4165000 ID_0.01_52 -0.0807515 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 4165000 4200000 ID_0.01_53 -0.088488 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 4200000 4220000 ID_0.01_54 -0.098724 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 4220000 4270000 ID_0.01_55 -0.088911 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 4270000 4365000 ID_0.01_56 -0.11633575 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 4365000 4405000 ID_0.01_57 -0.0944955 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 4405000 4490000 ID_0.01_58 -0.07463925 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 4490000 4625000 ID_0.01_59 0.00287075 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 4625000 4650000 ID_0.01_60 0.04064075 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 4650000 4790000 ID_0.01_61 0.03764975 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 4790000 4895000 ID_0.01_62 -0.06999725 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 4895000 5000000 ID_0.01_63 -0.076914 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 5000000 5110000 ID_0.01_64 -0.0378805 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 5110000 5240000 ID_0.01_65 -0.061049 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 5240000 5280000 ID_0.01_66 0.07173475 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 5280000 5360000 ID_0.01_67 0.02598475 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 5360000 5465000 ID_0.01_68 -0.06976425 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 5465000 5555000 ID_0.01_69 0.0082995 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 5555000 5575000 ID_0.01_70 -0.03433 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 5575000 5745000 ID_0.01_71 0.00900825 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 5745000 5815000 ID_0.01_72 -0.09901225 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 5815000 5875000 ID_0.01_73 -0.08504275 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 5875000 5960000 ID_0.01_74 -0.107036 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 5960000 5990000 ID_0.01_75 -0.0645035 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 5990000 6120000 ID_0.01_76 -0.06534175 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 6120000 6195000 ID_0.01_77 -0.06653425 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 6195000 6230000 ID_0.01_78 -0.08219225 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 6230000 6255000 ID_0.01_79 -0.07949925 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 6255000 6370000 ID_0.01_80 -0.0959415 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 6370000 6445000 ID_0.01_81 -0.0155925 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 6445000 6490000 ID_0.01_82 -0.0843135 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 6490000 6560000 ID_0.01_83 -0.07350925 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 6560000 6585000 ID_0.01_84 0.050254 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 6585000 6730000 ID_0.01_85 0.05181025 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 6730000 6875000 ID_0.01_86 -0.08674075 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 6875000 6960000 ID_0.01_87 0.015592 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 6960000 7075000 ID_0.01_88 -0.06386025 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 7075000 7120000 ID_0.01_89 -0.05008325 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 7120000 7145000 ID_0.01_90 -0.04982075 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 7145000 7305000 ID_0.01_91 -0.049721 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 7305000 7370000 ID_0.01_92 -0.10379175 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 7370000 7525000 ID_0.01_93 -0.0351445 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 7525000 7605000 ID_0.01_94 -0.05807975 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 7605000 7630000 ID_0.01_95 -0.02439625 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 7630000 7700000 ID_0.01_96 -0.0078695 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 7700000 7760000 ID_0.01_97 -0.05487375 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 7760000 7805000 ID_0.01_98 -0.0722705 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 7805000 7900000 ID_0.01_99 -0.048435 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 7900000 7950000 ID_0.01_100 -0.04267725 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 7950000 8010000 ID_0.01_101 -0.02681575 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 8010000 8055000 ID_0.01_102 -0.049908 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 8055000 8200000 ID_0.01_103 -0.077315 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 8200000 8305000 ID_0.01_104 -0.03326775 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 8305000 8340000 ID_0.01_105 -0.07717275 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 8340000 8410000 ID_0.01_106 -0.07715575 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 8410000 8435000 ID_0.01_107 -0.088482 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 8435000 8465000 ID_0.01_108 -0.098101 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 8465000 8505000 ID_0.01_109 -0.09699025 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 8505000 8645000 ID_0.01_110 -0.09547525 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 8645000 8670000 ID_0.01_111 0.015577 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 8670000 8710000 ID_0.01_112 0.00026425 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 8710000 8770000 ID_0.01_113 0.03299475 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 8770000 8855000 ID_0.01_114 0.05842025 . 1.0 1.0 1.0 0.0 0.0 0.0
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+chr3L 9225000 9355000 ID_0.01_119 -0.0200285 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 9355000 9395000 ID_0.01_120 -0.10868725 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 9395000 9485000 ID_0.01_121 -0.10117225 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 9485000 9605000 ID_0.01_122 -0.10105 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 9605000 9720000 ID_0.01_123 -0.0327885 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 9720000 9820000 ID_0.01_124 -0.10868725 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 9820000 9895000 ID_0.01_125 -0.0672575 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 9895000 9965000 ID_0.01_126 -0.1071045 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 9965000 10120000 ID_0.01_127 -0.10162625 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 10120000 10205000 ID_0.01_128 -0.02085 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 10205000 10320000 ID_0.01_129 -0.08171475 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 10320000 10445000 ID_0.01_130 -0.038513 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 10445000 10535000 ID_0.01_131 -0.04705425 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 10535000 10585000 ID_0.01_132 0.00456875 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 10585000 10685000 ID_0.01_133 -0.02505125 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 10685000 10740000 ID_0.01_134 0.08679725 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 10740000 10780000 ID_0.01_135 0.065835 . 1.0 1.0 1.0 0.0 0.0 0.0
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+chr3L 10885000 10960000 ID_0.01_138 -0.04725125 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 10960000 11070000 ID_0.01_139 0.03732375 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 11070000 11195000 ID_0.01_140 -0.088851 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 11195000 11230000 ID_0.01_141 -0.1098975 . 1.0 1.0 1.0 0.0 0.0 0.0
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+chr3L 11295000 11380000 ID_0.01_143 -0.05611625 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 11380000 11515000 ID_0.01_144 -0.02769625 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 11515000 11625000 ID_0.01_145 -0.1065995 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 11625000 11715000 ID_0.01_146 -0.090991 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 11715000 11785000 ID_0.01_147 -0.0141535 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 11785000 11825000 ID_0.01_148 -0.062442 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 11825000 11930000 ID_0.01_149 -0.0614325 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3L 11930000 11945000 ID_0.01_150 -0.041385 . 1.0 1.0 1.0 0.0 0.0 0.0
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+chr3L 11980000 12075000 ID_0.01_152 -0.0250355 . 1.0 1.0 1.0 0.0 0.0 0.0
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+chr3R 23185000 23195000 ID_0.01_1359 -0.00294725 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3R 23195000 23415000 ID_0.01_1360 -0.00275775 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3R 23415000 23560000 ID_0.01_1361 -0.090027 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3R 23560000 23770000 ID_0.01_1362 -0.104602 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3R 23770000 23815000 ID_0.01_1363 -0.1119105 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3R 23815000 23920000 ID_0.01_1364 -0.0660765 . 1.0 1.0 1.0 0.0 0.0 0.0
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+chr3R 24030000 24160000 ID_0.01_1366 -0.05579575 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3R 24160000 24205000 ID_0.01_1367 -0.01546725 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3R 24205000 24345000 ID_0.01_1368 -0.0326015 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3R 24345000 24375000 ID_0.01_1369 -0.0623065 . 1.0 1.0 1.0 0.0 0.0 0.0
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+chr3R 24450000 24625000 ID_0.01_1371 -0.09836075 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3R 24625000 24745000 ID_0.01_1372 -0.03171375 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3R 24745000 24885000 ID_0.01_1373 -0.08589625 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3R 24885000 24995000 ID_0.01_1374 -0.09323725 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3R 24995000 25090000 ID_0.01_1375 -0.0589785 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3R 25090000 25165000 ID_0.01_1376 0.03674225 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3R 25165000 25330000 ID_0.01_1377 -0.0462465 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3R 25330000 25405000 ID_0.01_1378 -0.08303325 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3R 25405000 25570000 ID_0.01_1379 -0.00546225 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3R 25570000 25580000 ID_0.01_1380 -0.04654075 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3R 25580000 25730000 ID_0.01_1381 -0.01871575 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3R 25730000 25880000 ID_0.01_1382 -0.00858875 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3R 25880000 25990000 ID_0.01_1383 -0.10581625 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3R 25990000 26050000 ID_0.01_1384 -0.090403 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3R 26050000 26180000 ID_0.01_1385 -0.0935315 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3R 26180000 26275000 ID_0.01_1386 -0.11469275 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3R 26275000 26330000 ID_0.01_1387 -0.1002735 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3R 26330000 26490000 ID_0.01_1388 -0.092304 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3R 26490000 26565000 ID_0.01_1389 0.0627965 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3R 26565000 26640000 ID_0.01_1390 -0.01974475 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3R 26640000 26715000 ID_0.01_1391 -0.07430725 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3R 26715000 26870000 ID_0.01_1392 -0.049789 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3R 26870000 27045000 ID_0.01_1393 -0.0249905 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3R 27045000 27155000 ID_0.01_1394 -0.074189 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3R 27155000 27185000 ID_0.01_1395 -0.00609925 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3R 27185000 27250000 ID_0.01_1396 -0.01281025 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3R 27250000 27385000 ID_0.01_1397 -0.04990275 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3R 27385000 27420000 ID_0.01_1398 -0.041305 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3R 27420000 27570000 ID_0.01_1399 -0.0499295 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3R 27570000 27700000 ID_0.01_1400 -0.08094325 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3R 27700000 27750000 ID_0.01_1401 -0.01535 . 1.0 1.0 1.0 0.0 0.0 0.0
+chr3R 27750000 27770000 ID_0.01_1402 0.01357725 . 1.0 nan 1.0 0.0 nan 0.0
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/hicInfo/hicInfo_output.txt
--- a/test-data/hicInfo/hicInfo_output.txt Tue Jan 10 19:05:09 2023 +0000
+++ b/test-data/hicInfo/hicInfo_output.txt Wed Oct 18 10:42:59 2023 +0000
@@ -1,8 +1,8 @@
-# Matrix information file. Created with HiCExplorer's hicInfo version 3.4
+# Matrix information file. Created with HiCExplorer's hicInfo version 3.7.2
File: matrix_name.h5
Size: 33,754
Bin_length: 5000
-Sum of matrix: 35778.0
+Sum of matrix: 37321.0
Chromosomes:length: chr2L: 23011544 bp; chr2LHet: 368872 bp; chr2R: 21146708 bp; chr2RHet: 3288761 bp; chr3L: 24543557 bp; chr3LHet: 2555491 bp; chr3R: 27905053 bp; chr3RHet: 2517507 bp; chr4: 1351857 bp; chrM: 19517 bp; chrUextra: 29004656 bp; chrU: 10049037 bp; chrX: 22422827 bp; chrXHet: 204112 bp; chrYHet: 347038 bp;
Non-zero elements: 69,213
Minimum (non zero): 1
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/hicInterIntraTAD/matrix.cool
Binary file test-data/hicInterIntraTAD/matrix.cool has changed
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/hicInterIntraTAD/output.txt
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicInterIntraTAD/output.txt Wed Oct 18 10:42:59 2023 +0000
@@ -0,0 +1,22 @@
+# Created with HiCExplorer's hicInterIntraTAD version 3.7.2
+# Chromosome start end name score strand inter_left_sum inter_right_sum inter_left_density inter_right_density inter_left_number_of_contacts inter_right_number_of_contacts inter_left_number_of_contacts_nnz inter_right_number_of_contacts_nnz intra_sum intra_number_of_contacts intra_number_of_contacts_nnz intra_density inter_left_intra_ratio inter_right_intra_ratio inter_left_inter_right_intra_ratio
+chr2 17100000 18100000 region_0 0 + 0 148.64980341892507 0 1.0 0 90 0 90 289.00804022517053 100 100 1.0 0.0 0.5143448718696884 0.5143448718696884
+chr2 18100000 19100000 region_1 0 + 162.1124908492847 211.04026046280666 1.0 1.0 100 140 100 140 277.9356647725957 100 100 1.0 0.583273438412172 0.7593133491359512 1.3425867875481232
+chr2 19100000 20600000 region_2 0 + 223.14353637851622 150.01947633135822 1.0 1.0 150 90 150 90 556.143932925097 225 225 1.0 0.4012334274777925 0.269749371430369 0.6709827989081616
+chr2 20600000 21300000 region_3 0 + 171.34866125986417 274.4679914622871 1.0 1.0 105 84 105 84 149.85761183392816 49 49 1.0 1.1434097952244984 1.8315251931710472 2.9749349883955456
+chr2 21300000 22600000 region_4 0 + 283.89289960594425 768.874984677404 1.0 1.0 91 208 91 208 24180.36424789467 169 169 1.0 0.011740637845464306 0.03179749390021485 0.04353813174567915
+chr2 22600000 24300000 region_5 0 + 789.804014201572 321.70053830625835 1.0 1.0 221 238 221 238 659.9593561049022 289 289 1.0 1.1967464464221198 0.48745507633219043 1.6842015227543101
+chr2 24300000 25800000 region_6 0 + 340.44705127228065 836.790681935677 1.0 1.0 255 720 255 720 598.8884085354028 225 225 1.0 0.5684649200422041 1.3972397361673277 1.965704656209532
+chr2 25800000 30700000 region_7 0 + 852.3657188383157 1593.0953595672838 1.0 1.0 735 1421 735 1421 4153.286346671477 2401 2401 1.0 0.20522681262307327 0.3835746506724779 0.5888014632955512
+chr2 30700000 33700000 region_8 0 + 1644.3620053137968 315.02407146145276 1.0 1.0 1470 240 1470 240 1873.0714290428866 900 900 1.0 0.8778960480722525 0.16818582920910052 1.046081877281353
+chr2 33700000 34600000 region_9 0 + 351.38600814451206 204.32883091037917 1.0 1.0 270 153 270 153 245.00889544594847 81 81 1.0 1.434176532672184 0.8339649486541041 2.268141481326288
+chr2 34600000 36400000 region_10 0 + 213.88883777381795 379.5343566721307 1.0 1.0 162 288 162 288 770.6376988509402 324 324 1.0 0.27754785172427593 0.49249388816305717 0.7700417398873332
+chr2 36400000 38100000 region_11 0 + 399.4783208321819 189.4340956757372 1.0 1.0 306 136 306 136 635.9658356069232 289 289 1.0 0.6281443097504547 0.29786835246417603 0.9260126622146307
+chr2 38100000 39000000 region_12 0 + 209.82145375215833 74.59004956153072 1.0 1.0 153 45 153 45 229.67774089590498 81 81 1.0 0.9135471854334115 0.3247595925951596 1.2383067780285713
+chr2 39000000 39600000 region_13 0 + 87.2296637584025 120.04828267162685 1.0 1.0 54 72 54 72 114.2377217834551 36 36 1.0 0.7635802114799864 1.0508637672168046 1.814443978696791
+chr2 39600000 40900000 region_14 0 + 127.68593516818584 348.8073054441913 1.0 1.0 78 247 78 247 447.58733970743407 169 169 1.0 0.2852760206569915 0.7793055667575172 1.0645815874145086
+chr2 40900000 42900000 region_15 0 + 363.6155543954171 330.73139298156053 1.0 1.0 260 240 260 240 912.1015373488856 400 400 1.0 0.3986568813953566 0.3626037008367121 0.7612605822320687
+chr2 42900000 44200000 region_16 0 + 353.76150800590995 305.3562724757596 1.0 1.0 260 208 260 208 434.0150296605763 169 169 1.0 0.8150904550069866 0.7035615165552332 1.51865197156222
+chr2 44200000 45900000 region_17 0 + 321.3851510623236 309.7368872510572 1.0 1.0 221 221 221 221 667.4121186463332 289 289 1.0 0.4815392799791639 0.4640863996885097 0.9456256796676736
+chr2 45900000 47300000 region_18 0 + 330.1441180225245 330.3028710611577 1.0 1.0 238 238 238 238 509.86032585858186 196 196 1.0 0.6475187444062777 0.6478301101481911 1.2953488545544687
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diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/hicInterIntraTAD/plot.png
Binary file test-data/hicInterIntraTAD/plot.png has changed
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/hicInterIntraTAD/untreated_R1_domains_chr1_chr2.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/hicInterIntraTAD/untreated_R1_domains_chr1_chr2.bed Wed Oct 18 10:42:59 2023 +0000
@@ -0,0 +1,20 @@
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+chr2 47300000 49100000 ID_0.01_29 -0.003388500000 . 47300000 49100000 31,120,180
\ No newline at end of file
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/hicMergeLoops/gm12878_all.bedgraph
--- a/test-data/hicMergeLoops/gm12878_all.bedgraph Tue Jan 10 19:05:09 2023 +0000
+++ b/test-data/hicMergeLoops/gm12878_all.bedgraph Wed Oct 18 10:42:59 2023 +0000
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diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/hicPCA/pca1_test1.bw
Binary file test-data/hicPCA/pca1_test1.bw has changed
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/hicPCA/pca1_test2.bw
Binary file test-data/hicPCA/pca1_test2.bw has changed
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/hicPCA/pca1_test3.bw
Binary file test-data/hicPCA/pca1_test3.bw has changed
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/hicPCA/pca2_test1.bw
Binary file test-data/hicPCA/pca2_test1.bw has changed
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/hicPCA/pca2_test2.bw
Binary file test-data/hicPCA/pca2_test2.bw has changed
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/hicPCA/pca2_test3.bw
Binary file test-data/hicPCA/pca2_test3.bw has changed
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/hicPlotDistVsCounts_result1.png
Binary file test-data/hicPlotDistVsCounts_result1.png has changed
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/hicPlotDistVsCounts_result2.png
Binary file test-data/hicPlotDistVsCounts_result2.png has changed
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/hicPlotMatrix/plot2.pdf
Binary file test-data/hicPlotMatrix/plot2.pdf has changed
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/hicPlotMatrix/plot3_pca.svg
--- a/test-data/hicPlotMatrix/plot3_pca.svg Tue Jan 10 19:05:09 2023 +0000
+++ b/test-data/hicPlotMatrix/plot3_pca.svg Wed Oct 18 10:42:59 2023 +0000
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diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/hicPlotSVL/p_values.txt
--- a/test-data/hicPlotSVL/p_values.txt Tue Jan 10 19:05:09 2023 +0000
+++ b/test-data/hicPlotSVL/p_values.txt Wed Oct 18 10:42:59 2023 +0000
@@ -1,4 +1,4 @@
-# Created with HiCExplorer's hicPlotSVL 3.6
+# Created with HiCExplorer's hicPlotSVL 3.7.2
# Short range vs long range contacts per chromosome, p-values of each distribution against each other distribution with Wilcoxon rank-sum
# Short range contacts: <= 2000000
0_small_test_matrix.h5 1_small_test_matrix.h5 1.0
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/hicPlotSVL/plot.png
Binary file test-data/hicPlotSVL/plot.png has changed
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/hicPlotSVL/ratios.txt
--- a/test-data/hicPlotSVL/ratios.txt Tue Jan 10 19:05:09 2023 +0000
+++ b/test-data/hicPlotSVL/ratios.txt Wed Oct 18 10:42:59 2023 +0000
@@ -1,4 +1,4 @@
-# Created with HiCExplorer's hicPlotSVL 3.6
+# Created with HiCExplorer's hicPlotSVL 3.7.2
# Short range vs long range contacts per chromosome: raw data
# Short range contacts: <= 2000000
# 0_small_test_matrix.h5 1_small_test_matrix.h5
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/hicQuickQC/QC.log
--- a/test-data/hicQuickQC/QC.log Tue Jan 10 19:05:09 2023 +0000
+++ b/test-data/hicQuickQC/QC.log Wed Oct 18 10:42:59 2023 +0000
@@ -1,5 +1,5 @@
-File /tmp/tmp12xmnm2f.h5
+File /var/folders/nm/9sgmbhhj6gn_h8b308xvhm0w0000gt/T/tmp8sucpx99.h5
Sequenced reads 983
Min rest. site distance 300
Max library insert size 1000
@@ -12,7 +12,7 @@
Low mapping quality 164 (16.68)
# count (percentage w.r.t. mappable, unique and high quality pairs)
-dangling end GATC 1 (0.33)
+dangling end GATC (restriction sequence GATC) 1 (0.33)
self ligation (removed) 0 (0.00)
One mate not close to rest site 0 (0.00)
same fragment 84 (28.00)
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/hicTADClassifier/predicted.txt
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/hicTADClassifier/predicted_second_classifier.txt
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/hicTADClassifier/unittest_classifier.BIN
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diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/hicTrainTADClassifier/model.BIN
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/hicTrainTADClassifier/multiFDR_dekker_domains.bed
--- /dev/null Thu Jan 01 00:00:00 1970 +0000
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\ No newline at end of file
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/hicTrainTADClassifier/small_test_matrix.cool
Binary file test-data/hicTrainTADClassifier/small_test_matrix.cool has changed
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/hicValidateLocations/overlap_smc3_matched_locations
--- a/test-data/hicValidateLocations/overlap_smc3_matched_locations Tue Jan 10 19:05:09 2023 +0000
+++ b/test-data/hicValidateLocations/overlap_smc3_matched_locations Wed Oct 18 10:42:59 2023 +0000
@@ -1,6 +1,6 @@
chr1 1050000 1060000 chr1 1180000 1190000 0.001
chr1 1710000 1720000 chr1 1830000 1840000 0.001
-chr1 1870000 1880000 chr1 3340000 3350000 0.0019430592210407133
+chr1 1870000 1880000 chr1 3340000 3350000 0.0019430592210407
chr1 2120000 2130000 chr1 2310000 2320000 0.001
chr1 2120000 2130000 chr1 2480000 2490000 0.001
chr1 2130000 2140000 chr1 3570000 3580000 0.001
@@ -79,7 +79,7 @@
chr1 29200000 29210000 chr1 29520000 29530000 0.001
chr1 29210000 29220000 chr1 29360000 29370000 0.001
chr1 29560000 29570000 chr1 31180000 31190000 0.001
-chr1 29560000 29570000 chr1 30580000 30590000 0.00321287751564984
+chr1 29560000 29570000 chr1 30580000 30590000 0.0032128775156498
chr1 30260000 30270000 chr1 30850000 30860000 0.001
chr1 31270000 31280000 chr1 31380000 31390000 0.001
chr1 31650000 31660000 chr1 32010000 32020000 0.001
@@ -96,7 +96,7 @@
chr1 35910000 35920000 chr1 36190000 36200000 0.001
chr1 36030000 36040000 chr1 36180000 36190000 0.001
chr1 36610000 36620000 chr1 36750000 36760000 0.001
-chr1 37040000 37050000 chr1 37780000 37790000 0.0030468037205961147
+chr1 37040000 37050000 chr1 37780000 37790000 0.0030468037205961
chr1 37160000 37170000 chr1 37780000 37790000 0.001
chr1 38020000 38030000 chr1 38140000 38150000 0.001
chr1 38490000 38500000 chr1 39050000 39060000 0.001
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/hicValidateLocations/overlap_smc3_statistics
--- a/test-data/hicValidateLocations/overlap_smc3_statistics Tue Jan 10 19:05:09 2023 +0000
+++ b/test-data/hicValidateLocations/overlap_smc3_statistics Wed Oct 18 10:42:59 2023 +0000
@@ -1,5 +1,5 @@
-# HiCExplorer hicValidateLocations 3.6
-# Overlap of loop file /tmp/tmpd80q3k6g/files/a/4/0/dataset_a40f2565-c94b-4e73-9b47-ec233d99bda8.dat with protein file /tmp/tmpd80q3k6g/files/7/1/1/dataset_7116b645-b87b-49a2-a957-3ebe53aba250.dat
+# HiCExplorer hicValidateLocations 3.7.2
+# Overlap of loop file /tmp/tmpjjk1hb59/files/a/8/9/dataset_a8916559-7d4d-42e7-b157-fdc26b57c5e2.dat with protein file /tmp/tmpjjk1hb59/files/e/5/a/dataset_e5ab267d-b489-4abc-88ce-c408eadfd25b.dat
#
Protein peaks: 3097
Matched Loops: 530
diff -r aeacaf08bd52 -r 2dccb6bb0add test-data/raw_qc_report
--- a/test-data/raw_qc_report Tue Jan 10 19:05:09 2023 +0000
+++ b/test-data/raw_qc_report Wed Oct 18 10:42:59 2023 +0000
@@ -1,5 +1,5 @@
-File matrix.h5
+File matrix.cool
Sequenced reads 983
Min rest. site distance 300
Max library insert size 1000
@@ -12,7 +12,7 @@
Low mapping quality 164 (16.68)
# count (percentage w.r.t. mappable, unique and high quality pairs)
-dangling end GATC 1 (0.33)
+dangling end GATC (restriction sequence GATC) 1 (0.33)
self ligation (removed) 0 (0.00)
One mate not close to rest site 0 (0.00)
same fragment 84 (28.00)